Amber 8 on Fujitsu VPP5000 Computers

Installation

Amber 8

configure script in the $AMBERHOME/src directory creates a configuration file, config.h, with the necessary options for complition and building. Configuration file can be examined and edited to match local environment. Below are samples of a config.h file for some Fujitsu platforms.

To install PMEMD one needs to generate a config.h file in the $AMBERHOME/src/pmemd directory by running configure script, i.e.

./configure <platform> <compiler> <parallel implementation>

and then enter the command 'make install'. To generate config.h file configure script uses files from the $AMBERHOME/src/pmemd/config_data directory. Below are samples of configuration files for some Fujitsu platforms.

Before Compiling ptraj

ptraj is a mixed C/Fortran program for analysing Molecular Dynamics results

To be compatible with a C/Fortran interface conventions a main module (in C language) of the ptraj program should be modified:

int

MAIN__(unsigned int argCount, char **argPointer)

/*main(unsigned int argCount, char **argPointer)*/

where the last line is the original (now commented) code.

Configuration files contain one of the best building options for the Fujitsu VPP Series computers equipped with the vector processor(s) which include, for example, VPP5000.